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eeg_nemar_preprocess.m
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eeg_nemar_preprocess.m
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% NEMAR preprocessing pipeline
% Required input:
% EEG - [struct] input dataset
% Optional inputs:
% pipeline - [cell] list of preprocessing steps in order
% logdir - [string] directory to log execution output
% resave - [boolean] whether to save processed data back on disk. Default true
% Output:
% EEG - [struct] processed dataset
% status - [boolean] whether dataset was processed successfully (1) or not (0)
% To do: ignore non-EEG channel types instead of removing them
function [EEG, status] = eeg_nemar_preprocess(EEG, varargin)
pipeline_all = {'check_import', 'check_chanloc', 'channelsystem', 'cleanraw', 'runica', 'iclabel'};
opt = finputcheck(varargin, { ...
'pipeline' 'cell' {} pipeline_all; ... % preprocessing steps
'logdir' 'string' {} './eeg_nemar_logs'; ...
'modeval' 'string' {'new', 'resume', 'rerun'} 'resume'; ... % if import mode, pipeline will overwrite existing outputdir. rerun won't
'resave' 'boolean' {} true; ...
}, 'eeg_nemar_preprocess');
if isstr(opt), error(opt); end
if ~exist(opt.logdir, 'dir')
logdirstatus = mkdir(opt.logdir);
end
try
which eeglab;
catch
try
addpath('/expanse/projects/nemar/eeglab');
eeglab nogui;
catch
error('EEGLAB load failed.')
end
end
resume = strcmp(opt.modeval, "resume");
[filepath, filename, ext] = fileparts(EEG.filename);
disp(filename)
log_file = fullfile(opt.logdir, filename);
if exist(log_file, 'file')
delete(log_file)
end
diary(log_file);
fprintf('Processing %s\n', fullfile(EEG.filepath, EEG.filename));
status_file = fullfile(opt.logdir, [filename '_preprocess.csv']);
% if status_file exists, read it
if exist(status_file, 'file') && (strcmp(opt.modeval, "resume") || strcmp(opt.modeval, "rerun"))
status_tbl = readtable(status_file);
else
status_tbl = array2table(zeros(1, numel(pipeline_all)));
status_tbl.Properties.VariableNames = pipeline_all;
writetable(status_tbl, status_file);
end
disp(status_tbl)
status = table2array(status_tbl);
splitted = split(EEG.filename(1:end-4),'_');
modality = splitted{end};
fprintf('Running pipeline sequence %s\n', strjoin(opt.pipeline, '->'));
try
for i=1:numel(opt.pipeline)
disp(fullfile(EEG.filepath, EEG.filename))
operation = opt.pipeline{i};
if strcmp(operation, "check_import")
% if check_import is not a field in status_tbl
if ~isfield(status_tbl, 'check_import')
status_tbl.check_import = status_tbl.remove_chan;
end
if resume && status_tbl.check_import
fprintf('Skipping check_import\n');
continue
end
if exist(fullfile(EEG.filepath, EEG.filename), 'file')
status_tbl.check_import = 1;
end
end
if strcmp(operation, "check_chanloc")
if resume && isfield(status_tbl, 'check_chanloc') && status_tbl.check_chanloc
fprintf('Skipping check_chanloc\n');
continue
end
if isfield(EEG.chanlocs, 'theta') && (strcmp(modality, 'eeg') || strcmp(modality, 'meg'))
thetas = [EEG.chanlocs.theta];
if isempty(thetas)
error("Error: No channel locations detected");
end
end
status_tbl.check_chanloc = 1;
end
if strcmp(operation, "remove_chan")
if resume && status_tbl.remove_chan
fprintf('Skipping remove_chan\n');
continue
end
% % remove non-ALLEEG channels (it is also possible to process ALLEEG data with non-ALLEEG data
% get non-EEG channels
% keep only EEG channels
rm_chan_types = {'AUDIO','EOG','ECG','EMG','EYEGAZE','GSR','HEOG','MISC','PPG','PUPIL','REF','RESP','SYSCLOCK','TEMP','TRIG','VEOG'};
if isfield(EEG.chanlocs, 'type')
EEG = pop_select(EEG, 'rmchantype', rm_chan_types);
if strcmp(modality, 'eeg')
types = {EEG.chanlocs.type};
eeg_indices = strmatch('EEG', types)';
if ~isempty(eeg_indices)
EEG = pop_select(EEG, 'chantype', 'EEG');
else
warning("No EEG channel type detected (for first EEG file). Keeping all channels");
end
end
else
warning("Channel type not detected (for first recording file)");
end
status_tbl.remove_chan = 1;
end
if strcmp(operation, "cleanraw")
if resume && status_tbl.cleanraw
fprintf('Skipping cleanraw\n');
continue
end
if EEG.trials > 1
error('Epoched data given to cleanraw');
end
% remove offset
EEG = pop_rmbase( EEG, [],[]);
% Highpass filter
EEG = pop_eegfiltnew(EEG, 'locutoff',0.5);
% clean data using the clean_rawdata plugin
options = {'FlatlineCriterion',4,'ChannelCriterion',0.85, ...
'LineNoiseCriterion',4,'Highpass', 'off' ,'BurstCriterion',20, ...
'WindowCriterion',0.25,'BurstRejection','on','Distance','Euclidian', ...
'WindowCriterionTolerances',[-Inf 7] ,'fusechanrej',1}; % based on Arnaud paper
EEG = pop_clean_rawdata( EEG, options{:});
status_tbl.cleanraw = 1;
end
if strcmp(operation, "runica")
if resume && status_tbl.runica
fprintf('Skipping runica\n');
continue
end
% run ICA reducing the dimention by 1 to account for average reference
K = 4; % TODO: use Arno's formula
if K >= 5
fprintf('Running amica\n');
options = {'batch', 1};
EEG = runamica17_nsg(EEG, options{:});
else
fprintf('Running extended ICA\n');
nChans = EEG.nbchan;
lrate = 0.00065/log(mean(nChans))/10; % not the runica default - suggested by Makoto approximately 12/22
options = {'icatype','runica','concatcond','on', 'extended', 1, 'lrate', 1e-5, 'maxsteps', 2000};
EEG = pop_runica(EEG, options{:});
end
status_tbl.runica = 1;
end
if strcmp(operation, "iclabel") && strcmp(modality, 'eeg')
if resume && status_tbl.iclabel
fprintf('Skipping iclabel\n');
continue
end
% % run ICLabel and flag artifactual components
% if strcmp(EEG.etc.datatype, 'EEG')
options = {'default'};
EEG = pop_iclabel(EEG, options{:});
options = {[NaN NaN;0.9 1;0.9 1;NaN NaN;NaN NaN;NaN NaN;NaN NaN]};
EEG = pop_icflag( EEG, options{:});
% end
status_tbl.iclabel = 1;
end
% if reached, operation completed without error and result should be saved
if opt.resave
if strcmp(opt.modeval, "new") || ~isfield(EEG.etc, 'nemar_pipeline_status')
EEG.etc.nemar_pipeline_status = status_tbl;
end
if strcmp(opt.modeval, "rerun") || strcmp(opt.modeval, "resume")
% iterate through fields of status_tbl and add to EEG.etc.nemar_pipeline_status
for j=1:numel(status_tbl.Properties.VariableNames)
field = status_tbl.Properties.VariableNames{j};
EEG.etc.nemar_pipeline_status.(field) = status_tbl.(field);
end
end
disp('Saving EEG file')
pop_saveset(EEG, 'filepath', EEG.filepath, 'filename', EEG.filename, 'savemode', 'onefile');
end
% write status file
writetable(status_tbl, status_file);
status = table2array(status_tbl);
end
catch ME
fprintf('%s\n%s\n',ME.identifier, ME.getReport());
end
% close log file
diary off
end